Align Xylose ABC transporter, periplasmic xylose-binding protein XylF (characterized, see rationale)
to candidate BWI76_RS14855 BWI76_RS14855 periplasmic binding protein/LacI transcriptional regulator
Query= uniprot:A0A0C4Y591 (325 letters) >FitnessBrowser__Koxy:BWI76_RS14855 Length = 317 Score = 223 bits (567), Expect = 6e-63 Identities = 122/316 (38%), Positives = 188/316 (59%), Gaps = 10/316 (3%) Query: 8 ALATAALSLLCTGAAAQSAPDAAPASAAAQRPLKKVGVTLGSLGNPYFVALAHGAEAAAK 67 A+A AA+ TG A AA A+ + + ++G+ + + NP+F A+ A+ AA Sbjct: 10 AIAVAAVITTMTGLAP-----AASAAPQESKKIARIGLMVQDMSNPFFSAMERNAKQAAA 64 Query: 68 KINPDAKVTVLSADYDLNKQFSHIDSFIVSKVDLILINAADARAIEPAVRKARKAGIVVV 127 KI A + V A DL Q + ID+FI KVDLI+I+A D IEPA+++A+ AGI+V+ Sbjct: 65 KIG--ATLNVQDAQVDLANQNTQIDAFIQQKVDLIIISAVDESGIEPAIQRAKAAGIIVI 122 Query: 128 AVDVAAAGADATVQTDNTRAGELACAFLAGRLGGRGNLIIQNGPPVSAVLDRVKGCKMVL 187 AVD A GADA + T+ +AGE +C +L ++GG+G +++ +G P+ ++DR+KGCK V Sbjct: 123 AVDTPAKGADAAIMTNAIQAGETSCEYLFSQMGGKGKVLLVDGTPIQTIIDRIKGCKNVA 182 Query: 188 GKHPGIHVLSDDQDGKGSREGGLNVMQLYLTRFPKIDAVFTINDPQAVGADLAARQLNR- 246 K+P I ++ Q + R GL V LT P + +F +NDP A+GA LA Q + Sbjct: 183 QKYPDIKIVG-QQASRNDRASGLMVTTDMLTANPDVSGIFGMNDPSALGAVLAVEQAGKA 241 Query: 247 GGILIASVDGAPD-IEAALKANTLVQASASQDPWAIARTAVEIGVGLMHGQAPANRTVLL 305 G I + VDG+P+ +E + + +A+Q+P + R A+ + ++ G+ A+RTVL+ Sbjct: 242 GAINVTGVDGSPEAVEELKRGGSPFIGTATQNPGEMVRQAISLAQDMVDGKPIASRTVLI 301 Query: 306 PPTLVTRANVNEYKGW 321 P LVTR NV Y GW Sbjct: 302 PSVLVTRDNVGSYPGW 317 Lambda K H 0.318 0.132 0.377 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 206 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 325 Length of database: 317 Length adjustment: 28 Effective length of query: 297 Effective length of database: 289 Effective search space: 85833 Effective search space used: 85833 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory